[ENH][BEP028] Specification update for BEP028 BIDS-Prov

mkdocs.yml

@@ -10,6 +10,7 @@ nav:
           - Data summary files: modality-agnostic-files/data-summary-files.md
           - Phenotypic and assessment data: modality-agnostic-files/phenotypic-and-assessment-data.md
           - Code: modality-agnostic-files/code.md
+          - Provenance: modality-agnostic-files/provenance.md
       - Modality specific files:
           - Magnetic Resonance Imaging: modality-specific-files/magnetic-resonance-imaging-data.md
           - Magnetoencephalography: modality-specific-files/magnetoencephalography.md

src/common-principles.md

@@ -355,10 +355,11 @@ Derivatives can be stored/distributed in two ways:
     it is RECOMMENDED to use the format `<pipeline>-<variant>` in cases where
     it is anticipated that the same pipeline will output more than one variant
     (for example, `AFNI-blurring` and `AFNI-noblurring`).
-    For the sake of consistency, the subdirectory name SHOULD be
-    the `GeneratedBy.Name` field in `dataset_description.json`,
-    optionally followed by a hyphen and a suffix (see
-    [Derived dataset and pipeline description][derived-dataset-description]).
+    For the sake of consistency, the subdirectory name MUST be
+    the `Name` field of the first `GeneratedBy` object in `dataset_description.json`,
+    optionally followed by a hyphen and a suffix.
+    That is, if a directory `<dataset>/derivatives/<pipeline>[-<variant>]/` is used, the first
+    `GeneratedBy` object should have a `Name` of `<pipeline>`.
 
     Example of derivatives with one directory per pipeline:
 

src/introduction.md

@@ -188,6 +188,12 @@ For example:
 
 -   (publication forthcoming)
 
+### Other extensions specific publications
+
+#### Provenance
+
+-   (publication forthcoming)
+
 ### Research Resource Identifier (RRID)
 
 BIDS has also a

src/modality-agnostic-files/dataset-description.md

@@ -16,7 +16,7 @@ A guide for using macros can be found at
 -->
 {{ MACROS___render_text("objects.files.dataset_description.description") }}
 
-Every dataset MUST include this file with the following fields:
+Every BIDS dataset MUST include this file with the following fields:
 
 <!-- This block generates a metadata table.
 The definitions of these fields can be found in
@@ -44,17 +44,6 @@ and a guide for using macros can be found at
    }
 ) }}
 
-Each object in the `GeneratedBy` array includes the following REQUIRED, RECOMMENDED
-and OPTIONAL keys:
-
-<!-- This block generates a table describing subfields within a metadata field.
-The definitions of these fields can be found in
-  src/schema/objects/metadata.yaml
-and a guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___make_subobject_table("metadata.GeneratedBy.items") }}
-
 Example:
 
 ```JSON
@@ -101,8 +90,6 @@ Example:
 }
 ```
 
-### Derived dataset and pipeline description
-
 As for any BIDS dataset, a `dataset_description.json` file MUST be found at the
 top level of every derived dataset:
 `<dataset>/derivatives/<pipeline_name>/dataset_description.json`.
@@ -122,11 +109,6 @@ and a guide for using macros can be found at
    }
 ) }}
 
-If a derived dataset is stored as a subdirectory of the raw dataset, then the `Name` field
-of the first `GeneratedBy` object MUST be a substring of the derived dataset directory name.
-That is, in a directory `<dataset>/derivatives/<pipeline>[-<variant>]/`, the first
-`GeneratedBy` object should have a `Name` of `<pipeline>`.
-
 Example:
 
 ```JSON

src/modality-agnostic-files/provenance-context.json

@@ -0,0 +1,48 @@
+{
+    "@context": {
+        "prov" : "http://www.w3.org/ns/prov#",
+        "xsd": "http://www.w3.org/2001/XMLSchema#",
+        "RRID": "http://scicrunch.org/resolver/",
+        "Id": "@id",
+        "Type": "@type",
+        "Label": "http://www.w3.org/2000/01/rdf-schema#label",
+        "StartedAtTime" : {
+          "@id": "prov:startedAtTime",
+          "@type": "http://www.w3.org/2001/XMLSchema#dateTime"
+        },
+        "EndedAtTime" : {
+          "@id": "prov:endedAtTime",
+          "@type": "xsd:dateTime"
+        },
+        "GeneratedBy" : {
+          "@id": "prov:wasGeneratedBy",
+          "@type": "@id"
+        },
+        "AttributedTo" : {
+          "@id": "prov:wasAttributedTo",
+          "@type": "@id"
+        },
+        "AssociatedWith" : {
+          "@id": "prov:wasAssociatedWith",
+          "@type": "@id"
+        },
+        "InformedBy" : {
+          "@id": "prov:wasInformedBy",
+          "@type": "@id"
+        },
+        "Used" : {
+          "@id": "prov:used",
+          "@type": "@id"
+        },
+        "ActedOnBehalfOf" : {
+          "@id": "prov:actedOnBehalfOf",
+          "@type": "@id"
+        },
+        "Entities": "prov:Entity",
+        "Entity": "prov:Entity",
+        "Activities": "prov:Activity",
+        "Activity": "prov:Activity",
+        "Software": "prov:SoftwareAgent",
+        "Atlocation": "prov:atLocation"
+    }
+}